We know that Palpatine created the Seperatist threat in order to gain his power; the chancellorship, war powers, clone army at his disposal, stripping of constitutional rights for the sake of securing the Republic, etc. The threat to the Republic from the Seperatist, and later supposedly by the Jedi, secured his power.

We know that he did not start the Rebel Alliance which later became a thorn in his side, that Mon Mothma and Bail Organa and others did.
But did he foresee that creation of a new threat to his power, and did he allow it in order to further ensure said power? Palpatine was nothing if not an innovator, revising his plans during the prequels when the need arose. We know also that he had the Death Star plans, and plans to build it, years before the Alliance was formed. So had he foreseen the Rebel Alliance? Had the Death Star been built specifically to destroy them, or had using it on them simply been an afterthought?

So when the rebel alliance arose as a threat not to civilian worlds as Dooku and Grievous were, but as a threat to Imperial ships and interests, did Palpatine allow it prior to the completion of the Death Star and the disbanding of the Senate, because it suited his purposes somehow?
So that is my query, in two parts: Just as Palpatine had allowed the rebels to gain the plans and location of the second Death Star, which suit his purpose and enabled him to try to destroy them, had he also enabled them to exist prior to that because it suited his purposes? Maybe Palpatine and/or Darth Vader made claims that the rebel alliance was the remnant of the defeated Seperatists. It would be very easy to cast the rebels in an evil light, not fighting to restore the Republic but threatening its people.

Second part:
The Seperatist armies were known throughout the Republic as evil war mongers rebelling against the Republic. So when the rebel alliance arose, fighting against the fleets of the New Order, how would they have assured the people they were fighting for, that they were fighting for them and not against them?

"Your focus determines your reality." --Qui-Gon Jinn
"Reality leaves a lot to the imagination." --John Lennon
"Imagination will often carry us to worlds that never were. But without it we go nowhere." --Carl Sagan

I feel that Palpatine had two separate events. His plan to take control up to the end of the Clone Wars. Then a separate plan when trying to destroy the Rebel Alliance (ie a plan to lure the Rebels to their death).

The movies had Palpatine as xenophobic as there was no aliens controlling his miltary. This gave the Rebel a chance to recruit.

Certainly, based solely on his actions and words, would one have any reason to doubt that all transpired according to his design...and I'd lump the rebellion in with that.
I mean, it's a bit of a stretch to come to that conclusion after seeing just the OT, but his puppeteering throughout the entire PT lends a lot of credence to this line of thought. Talk about your long game, though. But that's another one of his traits...immeasurable patience. Which is why it was a bit odd that he seemed to arguably rush along his plan to turn Luke in ROTJ.

"All right, look, there's only one "Return," okay, and it ain't "of the King," it's "of the Jedi."

Certainly, based solely on his actions and words, would one have any reason to doubt that all transpired according to his design...and I'd lump the rebellion in with that.
I mean, it's a bit of a stretch to come to that conclusion after seeing just the OT, but his puppeteering throughout the entire PT lends a lot of credence to this line of thought.

"Puppeteering" is very different from controlling every last occurrence, though. I like that you brought up going by his "actions and words", because that is important. Looking at ROTS, for example, he's clearly a liar. Everything he's spouting to Vader in his office is not just spin, but complete falsehoods. All that crap about the "plot" against them was nonsense since he was the one commanding the Separatists, and therefore acting treasonously against the Republic. And the Jedi were going to not only kill both of them but all of the senators? Never in a million years. So why should we trust his statement that everything transpired by his design?

There are clear examples of things not going his way:
**Maul losing to Obi-wan in TPM.
**The Trade Separation failing to get Amidala to sign over the planet to them.
**Vader getting his ass whupped on Mustafar and ending up a mechanical abomination in ROTS.
**The Death Star destruction in ANH.
**Luke's existence.
**Vader failing to capture Luke in ESB.
**Probably everything about the finale to ROTJ (Death Star destruction again, Anakin's return, Luke refusing to turn).

I'm sure there are plenty of other examples.

The reason for the Death Star was a show of force (no pun intended) to keep the star systems in line. There's nothing there that the Emperor would want by design. Meaning, to have to step up efforts to maintain control/obedience is only because the masses aren't. And to fail, spectacularly, with the DS being destroyed so quickly and the loss of Tarkin...yeah, that's not an intended design.

We know that he did not start the Rebel Alliance which later became a thorn in his side, that Mon Mothma and Bail Organa and others did.
But did he foresee that creation of a new threat to his power, and did he allow it in order to further ensure said power? Palpatine was nothing if not an innovator, revising his plans during the prequels when the need arose. We know also that he had the Death Star plans, and plans to build it, years before the Alliance was formed. So had he foreseen the Rebel Alliance? Had the Death Star been built specifically to destroy them, or had using it on them simply been an afterthought?

I'm not sure if it is now, or ever was canon, but in the Force Unleashed game, Vader and the Emperor manipulate your character in to helping bring the Alliance together so they can wipe out their enemies in "one swift stroke". So, he's kind of telling the truth when he says "even the Rebel Alliance" was part of his plan, but it definitely didn't go how he wanted. My impression was always that he was lying to make himself seem more powerful, and cover for the fact that the Alliance was an actual threat to his power, but there is a little truth to his words.

I'm not sure if it is now, or ever was canon, but in the Force Unleashed game, Vader and the Emperor manipulate your character in to helping bring the Alliance together so they can wipe out their enemies in "one swift stroke". So, he's kind of telling the truth when he says "even the Rebel Alliance" was part of his plan, but it definitely didn't go how he wanted. My impression was always that he was lying to make himself seem more powerful, and cover for the fact that the Alliance was an actual threat to his power, but there is a little truth to his words.

After ROTS it would seem your impression is correct. Palpatine in the PT was all about giving just enough information to manipulate someone to do his bidding. In light of all of that plus Rebels, I'd assume he's just taking credit for it with Luke in an effort to intimidate the boy.

"Your focus determines your reality." --Qui-Gon Jinn
"Reality leaves a lot to the imagination." --John Lennon
"Imagination will often carry us to worlds that never were. But without it we go nowhere." --Carl Sagan